Variant report

Variant	rs10498869
Chromosome Location	chr6:70456678-70456679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs13437057	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1457498	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs16868113	0.96[EUR][1000 genomes]
rs16868129	1.00[EUR][1000 genomes]
rs17503698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28434733	0.92[EUR][1000 genomes]
rs3799109	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4707324	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6936974	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs9294846	0.84[EUR][1000 genomes]
rs9294847	0.84[EUR][1000 genomes]
rs9294849	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9446157	0.92[EUR][1000 genomes]
rs9446159	0.96[EUR][1000 genomes]
rs9446161	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9454865	0.89[EUR][1000 genomes]
rs9454868	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs9454873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes]
rs9454876	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9454880	0.96[EUR][1000 genomes]
rs9454881	1.00[EUR][1000 genomes]
rs9454887	0.98[EUR][1000 genomes]
rs9454889	0.98[EUR][1000 genomes]
rs9454890	1.00[EUR][1000 genomes]
rs9454892	0.86[CEU][hapmap];0.93[EUR][1000 genomes]
rs9454893	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv830682	chr6:70397851-70592883	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv819863	chr6:70448447-70457777	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
4	esv3451372	chr6:70454531-70457929	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv970140	chr6:70456399-70456899	Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10498869	LMBRD1	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70380800-70467800	Weak transcription	K562	blood
2	chr6:70405000-70468400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:70406600-70457400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:70429000-70462400	Weak transcription	Colon Smooth Muscle	Colon
5	chr6:70429000-70467600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:70431400-70498600	Weak transcription	Ovary	ovary
7	chr6:70432000-70468200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:70432000-70470400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:70432000-70470400	Weak transcription	Gastric	stomach
10	chr6:70432000-70479800	Weak transcription	Pancreas	Pancrea
11	chr6:70432200-70480000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:70432600-70461600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:70435800-70498800	Weak transcription	Adipose Nuclei	Adipose
14	chr6:70436000-70457200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:70441200-70463400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:70442400-70498200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:70442400-70498400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:70443000-70468000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:70444800-70461000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:70445000-70458400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:70445200-70458800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:70445200-70458800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:70446000-70470400	Weak transcription	Psoas Muscle	Psoas
24	chr6:70447400-70459000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:70447800-70498400	Weak transcription	Placenta	Placenta
26	chr6:70448400-70458800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:70448400-70470600	Weak transcription	Right Ventricle	heart
28	chr6:70448800-70489800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:70450600-70472000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:70450800-70487600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:70453800-70468600	Weak transcription	Small Intestine	intestine
32	chr6:70453800-70505600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:70454800-70457200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:70454800-70459000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:70454800-70459800	Weak transcription	HMEC	breast
36	chr6:70455000-70457600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr6:70455000-70458200	Strong transcription	Fetal Thymus	thymus
38	chr6:70455200-70457800	Strong transcription	GM12878-XiMat	blood
39	chr6:70455400-70456800	Strong transcription	Left Ventricle	heart
40	chr6:70455400-70457600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:70455400-70458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:70455400-70459400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:70455600-70456800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:70455600-70457200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:70455600-70457200	Strong transcription	Liver	Liver
46	chr6:70455600-70457200	Strong transcription	Fetal Brain Female	brain
47	chr6:70455600-70457200	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:70455600-70457200	Strong transcription	Fetal Stomach	stomach
49	chr6:70455600-70457400	Strong transcription	Primary T cells from cord blood	blood
50	chr6:70455600-70457400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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